How to use the pygtftk.arg_formatter.FileWithExtension function in pygtftk

parser_grp = parser.add_argument_group('Arguments')

    # required but not required...

    parser_grp.add_argument(
        'bed_list',
        help='A list of bed files for H3K4me3.',
        type=bedFileWithUnambiguousNames(),
        nargs='+')

    parser_grp.add_argument('-i', '--inputfile',
                            help="The input GTF file.",
                            default=sys.stdin,
                            metavar="GTF",
                            required=False,
                            type=FileWithExtension('r',
                                                   valid_extensions='\.[Gg][Tt][Ff](\.[Gg][Zz])?$'))

    parser_grp.add_argument('-o', '--outputfile',
                            help="Output file.",
                            default=sys.stdout,
                            metavar="TXT",
                            type=FileWithExtension('w',
                                                   valid_extensions=('\.[Tt][Xx][Tt]',
                                                                     '\.[Cc][Ss][Vv]',
                                                                     '\.[Tt][Aa][Bb]',
                                                                     '\.[Tt][Ss][Vv]',
                                                                     '\.[Cc][Oo][Vv]')))

    parser_grp.add_argument('-l', '--labels',
                            help='Bed labels.',
                            default=None,

parser_grp.add_argument('-i', '--inputfile',
                            help="The input GTF/BED file. Only GTF file if  is used.",
                            default=sys.stdin,
                            metavar="GTF/BED",
                            required=False,
                            type=FileWithExtension('r',
                                                   valid_extensions=('\.[Gg][Tt][Ff](\.[Gg][Zz])?$',
                                                                     '\.[Bb][Ee][Dd]$',
                                                                     '\.[Bb][Ee][Dd]3$',
                                                                     '\.[Bb][Ee][Dd]6$')))

    parser_grp.add_argument('-o', '--outputfile',
                            help="Output file.",
                            default=sys.stdout,
                            metavar="TXT",
                            type=FileWithExtension('w',
                                                   valid_extensions=('\.[Tt][Xx][Tt]$',
                                                                     '\.[Cc][Ss][Vv]$',
                                                                     '\.[Tt][Aa][Bb]$',
                                                                     '\.[Tt][Ss][Vv]$',
                                                                     '\.[Cc][Oo][Vv]$',
                                                                     '\.[Bb][Ee][Dd]$')))
    parser_grp.add_argument(
        '-c', '--chrom-info',
        help="Tabulated two-columns file. Chromosomes"
             " as column 1 and sizes as"
             " column 2 ",
        default=None,
        metavar="CHROMINFO",
        action=checkChromFile,
        required=True)

parser_grp = parser.add_argument_group('Arguments')

    # required but not required...

    parser_grp.add_argument(
        'bw_list',
        help='A list of Bigwig files (last argument).',
        type=argparse.FileType('r'),
        nargs='+')

    parser_grp.add_argument('-i', '--inputfile',
                            help="The input GTF/BED file. Only GTF file if  is used.",
                            default=sys.stdin,
                            metavar="GTF/BED",
                            required=False,
                            type=FileWithExtension('r',
                                                   valid_extensions=('\.[Gg][Tt][Ff](\.[Gg][Zz])?$',
                                                                     '\.[Bb][Ee][Dd]$',
                                                                     '\.[Bb][Ee][Dd]3$',
                                                                     '\.[Bb][Ee][Dd]6$')))

    parser_grp.add_argument('-o', '--outputfile',
                            help="Output file.",
                            default=sys.stdout,
                            metavar="TXT",
                            type=FileWithExtension('w',
                                                   valid_extensions=('\.[Tt][Xx][Tt]$',
                                                                     '\.[Cc][Ss][Vv]$',
                                                                     '\.[Tt][Aa][Bb]$',
                                                                     '\.[Tt][Ss][Vv]$',
                                                                     '\.[Cc][Oo][Vv]$',
                                                                     '\.[Bb][Ee][Dd]$')))

def make_parser():
    """The main parser."""

    parser = argparse.ArgumentParser(add_help=True)

    parser_grp = parser.add_argument_group('Arguments')

    parser_grp.add_argument('-i', '--inputfile',
                            help='A zip file containing a matrix as produced by mk_matrix.',
                            default=None,
                            metavar='MATRIX',
                            type=FileWithExtension('r', '\.[Zz][Ii][Pp]'),
                            required=True)

    parser_grp.add_argument('-o', '--out-dir',
                            help='Output directory name.',
                            default="draw_profile",
                            metavar="DIR",
                            type=str)

    parser_grp.add_argument('-t', '--transcript-file',
                            help="A two columns file with the transcripts"
                                 " of interest and their classes.",
                            default=None,
                            type=argparse.FileType("r"),
                            required=False)

    parser_grp.add_argument('-s', '--stat',

# required but not required...

    parser_grp.add_argument('-i', '--inputfile',
                            help="The input GTF file.",
                            default=sys.stdin,
                            metavar="GTF",
                            required=False,
                            type=FileWithExtension('r',
                                                   valid_extensions='\.[Gg][Tt][Ff](\.[Gg][Zz])?$'))

    parser_grp.add_argument('-o', '--outputfile',
                            help="Output file.",
                            default=sys.stdout,
                            metavar="TXT",
                            type=FileWithExtension('w',
                                                   valid_extensions=('\.[Tt][Xx][Tt]',
                                                                     '\.[Cc][Ss][Vv]',
                                                                     '\.[Tt][Aa][Bb]',
                                                                     '\.[Tt][Ss][Vv]',
                                                                     '\.[Cc][Oo][Vv]')))

    parser_grp.add_argument('-b', '--bed-list',
                            help='A list of bed files for H3K4me3 epigenetic mark.',
                            type=bedFileWithUnambiguousNames(),
                            nargs='+',
                            required=True)

    parser_grp.add_argument('-w', '--bigwig_list',
                            help='A list of bigwigs files for H3K4me3 epigenetic mark.',
                            type=argparse.FileType('r'),
                            nargs='+')

def make_parser():
    """The main parser."""

    parser = argparse.ArgumentParser(add_help=True)

    parser_grp = parser.add_argument_group('Arguments')

    parser_grp.add_argument('-i', '--inputfile',
                            help='A zipped of matrix file as produced by mk_matrix.',
                            default=None,
                            metavar='MATRIX',
                            type=FileWithExtension('r', '\.[Zz][Ii][Pp]'),
                            required=True)

    parser_grp.add_argument('-o', '--out-dir',
                            help='Output directory name.',
                            default="heatmap_gtftk",
                            type=str)

    parser_grp.add_argument('-t', '--transcript-file',
                            help="A two columns file with the transcripts"
                                 " of interest and their classes.",
                            default=None,
                            type=argparse.FileType("r"),
                            required=False)

    parser_grp.add_argument('-s', '--order-fun',
                            help="The statistics used for row ordering.",

type=bedFileWithUnambiguousNames(),
        nargs='+')

    parser_grp.add_argument('-i', '--inputfile',
                            help="The input GTF file.",
                            default=sys.stdin,
                            metavar="GTF",
                            required=False,
                            type=FileWithExtension('r',
                                                   valid_extensions='\.[Gg][Tt][Ff](\.[Gg][Zz])?$'))

    parser_grp.add_argument('-o', '--outputfile',
                            help="Output file.",
                            default=sys.stdout,
                            metavar="TXT",
                            type=FileWithExtension('w',
                                                   valid_extensions=('\.[Tt][Xx][Tt]',
                                                                     '\.[Cc][Ss][Vv]',
                                                                     '\.[Tt][Aa][Bb]',
                                                                     '\.[Tt][Ss][Vv]',
                                                                     '\.[Cc][Oo][Vv]')))

    parser_grp.add_argument('-l', '--labels',
                            help='Bed labels.',
                            default=None,
                            type=str,
                            required=False)

    parser_grp.add_argument('-m', '--dist-min',
                            help='Minimum distance between two TSSs for them to be tested.',
                            default=0,
                            type=int,